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- PDB-4k2h: Crystal structure of C103A mutant of DJ-1 superfamily protein STM... -

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Basic information

Entry
Database: PDB / ID: 4k2h
TitleCrystal structure of C103A mutant of DJ-1 superfamily protein STM1931 from Salmonella typhimurium
ComponentsIntracellular protease/amidase
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / protein deglycase activity / peptidase activity / metal ion binding / cytosol
Similarity search - Function
DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative intracellular protease/amidase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsShumilin, I.A. / Niedzialkowska, E. / Domagalski, M.J. / Stam, J. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of C103A mutant of DJ-1 superfamily protein STM1931 from Salmonella typhimurium
Authors: Shumilin, I.A. / Niedzialkowska, E. / Domagalski, M.J. / Stam, J. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intracellular protease/amidase
B: Intracellular protease/amidase
C: Intracellular protease/amidase
D: Intracellular protease/amidase
E: Intracellular protease/amidase
F: Intracellular protease/amidase
G: Intracellular protease/amidase
H: Intracellular protease/amidase
I: Intracellular protease/amidase
J: Intracellular protease/amidase
K: Intracellular protease/amidase
L: Intracellular protease/amidase
M: Intracellular protease/amidase
N: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,11528
Polymers279,20014
Non-polymers91614
Water21,3121183
1
A: Intracellular protease/amidase
B: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-97 kcal/mol
Surface area13950 Å2
MethodPISA
2
C: Intracellular protease/amidase
D: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-97 kcal/mol
Surface area14040 Å2
MethodPISA
3
E: Intracellular protease/amidase
F: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-97 kcal/mol
Surface area13690 Å2
MethodPISA
4
G: Intracellular protease/amidase
H: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-96 kcal/mol
Surface area13860 Å2
MethodPISA
5
I: Intracellular protease/amidase
J: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-96 kcal/mol
Surface area13570 Å2
MethodPISA
6
K: Intracellular protease/amidase
L: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-95 kcal/mol
Surface area13560 Å2
MethodPISA
7
M: Intracellular protease/amidase
N: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-96 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.662, 113.751, 175.710
Angle α, β, γ (deg.)90.000, 109.330, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Intracellular protease/amidase


Mass: 19942.830 Da / Num. of mol.: 14 / Mutation: C103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: araH, STM1931 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8ZNU7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M bis-tris propane, 0.9M DL-malic acid, 0.005M zinc chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2012 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 169402 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.069 / Χ2: 2.111 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2420.4184941.207196.1
2.24-2.2820.37185231.231196
2.28-2.3220.33685621.304196.1
2.32-2.3720.32885181.301195.9
2.37-2.4220.28285191.32195.7
2.42-2.4820.24685791.434196.1
2.48-2.5420.22584971.541195.7
2.54-2.6120.18484831.652195.7
2.61-2.6920.16785131.79195.2
2.69-2.772.10.14684811.852195.2
2.77-2.872.10.12984591.967195
2.87-2.992.10.11684302.147195
2.99-3.122.10.09684502.45194.2
3.12-3.2920.08283652.628193.7
3.29-3.4920.07583152.976193.1
3.49-3.7620.06583003.209193.2
3.76-4.1420.05683363.197193.1
4.14-4.7420.04984293.241194.1
4.74-5.972.10.04486402.828195.9
5.97-502.40.04185092.784193.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E08
Resolution: 2.2→36.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1966 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8492 / SU B: 9.886 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2141 / SU Rfree: 0.1722 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 8016 5 %RANDOM
Rwork0.1715 ---
obs0.1731 160372 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 116.41 Å2 / Biso mean: 42.6984 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å2-2.01 Å2
2---1.05 Å2-0 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19400 0 14 1183 20597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01920028
X-RAY DIFFRACTIONr_bond_other_d00.0219547
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9727346
X-RAY DIFFRACTIONr_angle_other_deg3.62344832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64952636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09323.341823
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.913153092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2915148
X-RAY DIFFRACTIONr_chiral_restr0.0760.23171
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122941
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024399
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 583 -
Rwork0.242 11399 -
all-11982 -
obs--96.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1379-0.76750.30830.5662-0.01980.99030.034-0.0054-0.0328-0.03250.02650.01420.04830.0707-0.06050.09630.00930.06930.18350.01440.104584.3160.326-18.956
21.40480.01570.85941.16950.25310.58840.02310.18220.1604-0.1268-0.0901-0.1698-0.00890.14070.0670.0980.02120.09440.22680.04920.107593.6348.605-26.457
31.41820.11210.15951.25120.30880.22380.0201-0.04730.03610.0120.00810.09970.0290.0388-0.02820.1085-0.01640.06890.17040.0290.115467.48311.976-16.535
40.65490.02890.19240.1707-0.16990.4513-0.03850.08380.1012-0.0134-0.00560.0624-0.00550.04310.04410.1084-0.01380.06980.16450.03460.132665.15620.904-27.044
51.8493-0.84090.70163.3391-2.39761.73920.0031-0.08620.0524-0.0486-0.0893-0.11460.03440.01150.08620.1109-0.02120.07360.1863-0.05160.106630.63114.102-28.12
60.7943-0.05230.27210.25110.08980.23770.0129-0.06990.0577-0.001-0.0076-0.04210.0214-0.0599-0.00530.10330.00320.07590.1627-0.03510.123832.2618.285-23.222
71.08910.72790.4430.56110.1380.82480.0729-0.10920.0250.0105-0.03050.00740.0915-0.068-0.04240.0991-0.04370.07240.18470.00910.103611.0570.693-27.84
81.8574-0.0541.44780.867-0.1571.15050.0624-0.27790.19920.1801-0.17460.17860.0044-0.19390.11220.1027-0.04930.10070.2342-0.05670.11075.57210.708-17.875
90.9894-0.00270.59840.28880.03241.0520.04210.0183-0.04020.0271-0.02820.0281-0.09740.0618-0.01390.1032-0.03830.07430.15520.04030.1127-13.136-7.42-43.34
101.3212-0.13240.49330.63080.08940.48430.1632-0.001-0.10690.0917-0.06020.02190.1286-0.0195-0.1030.1079-0.01520.05590.15920.06280.1516-16.978-20.648-37.736
111.0703-0.08230.7550.07320.08881.41570.05590.0105-0.0889-0.0343-0.02320.06910.02480.0488-0.03260.10350.03630.01770.15-0.02710.1292-24.2-14.387-66.906
121.6549-0.08460.34760.0587-0.29851.5860.1642-0.1089-0.3592-0.06880.00410.0490.3923-0.066-0.16830.1522-0.0149-0.00430.0816-0.00980.1745-27.128-27.872-60.888
131.5019-0.6210.40521.0615-0.18380.33760.05090.03990.00910.0320.0673-0.02260.08410.0369-0.11820.0690.03820.00690.1556-0.03980.1322-45.357-9.288-87.189
143.545-0.02881.54811.5337-0.36920.90080.32250.5081-0.1107-0.3971-0.1913-0.25490.21420.3326-0.13120.13760.10550.06790.244-0.09090.1971-38.637-11.77-100.287
151.5630.66310.89911.34150.58240.70750.0002-0.07460.12120.04870.03830.02630.0312-0.0344-0.03850.03240.00330.03410.144-0.04130.1818-59.6738.195-67.127
162.44230.29251.00491.4741-0.39770.64040.3109-0.5930.29590.5145-0.30350.285-0.0145-0.169-0.00740.2406-0.10710.11030.2841-0.08630.1165-66.495.815-54.128
171.6714-0.51470.10280.2657-0.12450.5077-0.0171-0.0101-0.0474-0.002-0.08790.0577-0.06230.00440.1050.06440.00690.0440.1433-0.04410.1807-31.20114.114-59.517
181.6444-0.02250.21240.1543-0.2880.89210.001-0.00310.33080.0243-0.08470.0225-0.23080.02290.08370.13010.05740.00380.0987-0.05670.2006-30.05428.902-61.058
191.2544-0.03950.08930.31580.06210.4914-0.01380.0535-0.0136-0.022-0.0640.0237-0.02340.09780.07780.0794-0.01730.06840.18120.05720.1096-5.22711.483-65.46
201.4477-0.0890.550.15270.21010.86770.00570.16640.424-0.0226-0.064-0.078-0.15580.02610.05830.1328-0.07220.0250.14510.10240.1818-4.22826.273-67.162
212.0443-0.51461.29371.5202-0.99471.18410.08470.2536-0.0101-0.0464-0.00490.07590.0820.1131-0.07980.06990.02720.04150.21740.01410.088422.0323.883-56.137
224.5609-0.45192.40932.4930.52131.50880.71331.2813-0.1071-0.6921-0.5701-0.23680.19130.5408-0.14320.29860.26950.07260.508-0.03090.05529.683-0.745-68.24
231.9601-0.58020.86851.2782-0.56010.48380.18960.0623-0.2215-0.0247-0.03990.07210.07060.0519-0.14970.12910.05140.00070.1368-0.07270.161137.321-12.676-41.306
244.65140.07361.7611.6585-0.0670.69760.37470.4338-0.2264-0.4074-0.2503-0.24310.21510.2299-0.12440.23010.1707-0.020.2518-0.1570.218644.079-17.373-53.856
250.9299-0.32930.08810.48180.1341.15050.05840.0018-0.0686-0.08330.02360.13910.01610.1235-0.0820.1129-0.03030.01880.15150.02940.124462.92-14.022-17.85
260.84180.1590.27390.13990.24821.33490.0708-0.0461-0.1508-0.0087-0.0180.07830.2548-0.0407-0.05280.1567-0.0182-0.04110.11380.00460.216854.061-24.846-17.726
273.6415-0.2803-2.37220.39031.12693.99740.03920.01920.0957-0.00020.05120.0048-0.02620.0657-0.09040.1144-0.03340.0590.15410.08660.122665.566-9.1921.402
280.53540.11120.31790.28470.12260.60680.029-0.04-0.04160.02160.02020.04090.01420.053-0.04920.0919-0.03720.07260.18390.05790.119267.326-13.456.143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 88
2X-RAY DIFFRACTION2A89 - 185
3X-RAY DIFFRACTION3B1 - 61
4X-RAY DIFFRACTION4B62 - 185
5X-RAY DIFFRACTION5C1 - 18
6X-RAY DIFFRACTION6C19 - 185
7X-RAY DIFFRACTION7D0 - 115
8X-RAY DIFFRACTION8D116 - 185
9X-RAY DIFFRACTION9E1 - 114
10X-RAY DIFFRACTION10E115 - 185
11X-RAY DIFFRACTION11F1 - 116
12X-RAY DIFFRACTION12F117 - 185
13X-RAY DIFFRACTION13G0 - 114
14X-RAY DIFFRACTION14G115 - 185
15X-RAY DIFFRACTION15H1 - 114
16X-RAY DIFFRACTION16H115 - 185
17X-RAY DIFFRACTION17I1 - 114
18X-RAY DIFFRACTION18I115 - 185
19X-RAY DIFFRACTION19J1 - 114
20X-RAY DIFFRACTION20J115 - 185
21X-RAY DIFFRACTION21K1 - 116
22X-RAY DIFFRACTION22K117 - 185
23X-RAY DIFFRACTION23L1 - 114
24X-RAY DIFFRACTION24L115 - 185
25X-RAY DIFFRACTION25M1 - 62
26X-RAY DIFFRACTION26M63 - 185
27X-RAY DIFFRACTION27N1 - 18
28X-RAY DIFFRACTION28N19 - 185

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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